The 1GB GTX 460 is much better. Not only does the 768MB version obviously lose in VRAM, but the "SE" on the end of the 768MB version means it's underclocked for lower speed (and lower power consumption, but there are better cards for that now anyway). The higher bandwidth on the 1GB version will also allow it to scale up with antialiasing and higher resolutions without losing as much performance. The normal 1GB GTX 460 is overall the much stronger card.
I used to have a 768MB GTX 460 GC (factory overclocked, rather than underclocked), and I got rid of it about a year ago. If I had the 1GB version I wouldn't even have sold it yet, I'd still be using it.
Having said that, you should only buy either of them if you can get them for quite a low price. There are newer cards available, after all.